QwikMD Spotlights

The 2.12 release of
the molecular dynamics program NAMD
provides major enhancements in performance, flexibility, and accuracy,
complementing the greatly enhanced usability provided by the
QwikMD GUI released in
VMD 1.9.3.
NVIDIA GPU-accelerated simulations with NAMD 2.12 are up to three times as
fast as 2.11, particularly for implicit solvent simulations and
single-node simulations of smaller systems.
NAMD 2.12 is also optimized for the new Intel Xeon Phi KNL processors found in
Argonne Theta,
NERSC Cori,
and
TACC Stampede 2.
NAMD 2.12 builds on the asynchronous multi-copy scripting capabilities introduced in
NAMD 2.11
with the ability to modify and reload the molecular structure,
enabling development of grand canonical and constant pH ensemble methods,
as well as an optional Python interface for advanced on-the-fly analysis.
Finally, NAMD 2.12 provides a complete, no-recompilation-needed
interface for hybrid QM/MM
with both the semi-empirical code MOPAC and the ab initio/DFT code ORCA.
More on new features in the 2.12 release of NAMD can be found
here.
NAMD is available free-of-charge as source code, precompiled binaries,
pre-installed at supercomputer centers, and now jointly with VMD as
one-click interactive molecular modeling
on the Amazon cloud.

The latest release of VMD brings many
advances that help researchers prepare, analyze, and visualize
molecular simulations.
The new
QwikMD plugin
streamlines key simulation preparation and analysis tasks, and guides users
in the creation of reusable simulation workflows and protocols.
VMD now includes several advanced features for parallel analysis
and visualization of cellular-scale simulations, as
reported here,
and here.
VMD 1.9.3 strengthens collaboration between experimental and computational
biologists by supporting a broader range of experimental density map
image formats, such as those used in cryo-electron tomography.
Many updated plugins are included in VMD 1.9.3, including tools for
analysis of free energy perturbation simulations,
MDFF hybrid structure fitting,
ffTK force field parameterization,
and
normal mode analysis.
VMD 1.9.3 adds support for new hardware and operating system
platforms including
IBM OpenPOWER (ORNL Summit),
a variety of GPU-accelerated ARM SoCs,
the Amazon AWS EC2 cloud,
and most recently, the Intel Xeon Phi Knight's Landing many-core CPU (TACC Stampede 2, Argonne Theta).
The VMD 1.9.3 release adds stunning graphics produced using
interactive ray tracing using the latest multi-core CPUs and GPU accelerators,
enabling 360-degree panoramic movie rendering for VR headsets,
as
reported here,
and here.
Interactive ray tracing makes the task of getting a molecular
image "just right" much easier than ever before; it also enables
rendering of spectacular movies for communication of scientific results.
A VR movie rendering tutorial
assists users with the steps required in rendering and encoding
VR movies for upload to YouTube for display using VR headsets such
as Google Cardboard, Oculus Rift, and GearVR.
More details about VMD 1.9.3 features can be found
here.

Everything that living things do can be understood in terms of jigglings and wigglings of atoms.
Richard Feynman's remark in the early 1960's summarizes what is today widely accepted, namely,
that molecular processes can be described by the dynamics of biological molecules, therefore connecting
protein dynamics to biological function. Molecular dynamics (MD) is by far the best tool to investigate
jigglings and wigglings of biological systems. Advances in both software and hardware
have spread the use of MD, however the steepness of the learning curve of the methodology of MD
remains high. To assist new users in overcoming the initial barrier to use MD software, and to help the more advanced users to
speed up tedious steps, we have developed the QwikMD software, as decribed in a recent paper.
By incorporating an easy-to-use point-and-click user interface that connects the widely used molecular graphics
program VMD
with the powerful MD program NAMD,
QwikMD allows its users to prepare both basic and advanced MD simulations in just a few minutes. At the same time,
QwikMD keeps track of every step performed during the preparation of the simulation, allowing easy reproducibility
and shareability of protocols. More information about QwikMD, as well as introductory tutorials are available on our
QwikMD webpage.
QwikMD is available in VMD 1.9.3 or later versions.

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Protein Recycling (August 2016)

While waste recycling in daily life has become popular only recently,
living cells have been recycling their protein content since
the very beginning. Recycling of unneeded protein molecules in cells
is performed by a molecular machine called the proteasome, which cuts these
proteins into smaller pieces for reuse as building blocks for new proteins.
Proteins that need to be recycled are labeled by tags made of poly-ubiquitin
protein chains. The proteasome machine recognizes and binds to these tags,
pulls the tagged protein close, then unwinds it, and finally cuts it into
pieces. Despite its substantial role in the cell's life cycle, the
proteasome's atomic structure and function still remain elusive. In our
recent
study,
we obtained an atomic structure of the human 26S proteasome by combining
computational modeling techniques,
through molecular dynamics flexible fitting (MDFF) of the cryo-electron microscopy (cryo-EM) data.
The features observed in the resulting structure are important for coordinating
the proteasomal subunits during protein recycling.
One of the key advances is that for the first time the nucleotides
bound to the ATPase motor of the proteasome are resolved.
The atomic resolution of the structure
permits to perform molecular dynamics simulations to investigate the detailed proteasomal function,
in particular the protein unwinding process of the ATPase motor.
Furthermore, our obtained structure will serve as a
starting point for structure-guided drug discovery,
developing the proteasome as a crucial drug target.
The atomic models are deposited in the protein
data bank (PDB) with the PDB IDs 5L4G and 5L4K and the 3.9 Å resolution
cryo-EM density is deposited in the electron microscopy data bank
EMD-4002.
More information about our proteasome projects is available on our
proteasome website. Easy access to our modeling techniques is provided through
QwikMD, which was employed here for the first time.